Merge remote-tracking branch 'origin/master' into post-patch-update

CHANGELOG.md

@@ -19,6 +19,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
 - [#285](https://github.com/nf-core/taxprofiler/pull/285/files) Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
 - [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
+## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
+
+### `Added`
+
+### `Fixed`
+
+- [#291](https://github.com/nf-core/taxprofiler/pull/291) - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)
 
 ### `Dependencies`
 

README.md

@@ -1,6 +1,6 @@
 # ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7728364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7728364)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -112,8 +112,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

conf/modules.config

@@ -641,7 +641,6 @@ process {
         ext.args =  {
             [
                 "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
-                params.taxpasta_taxonomy_dir ? "--taxonomy ${params.taxpasta_taxonomy_dir}" : "",
                 params.taxpasta_add_name ?  "--add-name" : "",
                 params.taxpasta_add_rank ? "--add-rank" : "",
                 params.taxpasta_add_lineage ? "--add-lineage" : "",

lib/WorkflowMain.groovy

@@ -9,9 +9,8 @@ class WorkflowMain {
     //
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            // TODO nf-core: Add Zenodo DOI for pipeline after first release
-            //"* The pipeline\n" +
-            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
+            "* The pipeline\n" +
+            "  https://doi.org/10.5281/zenodo.7728364\n\n" +
             '* The nf-core framework\n' +
             '  https://doi.org/10.1038/s41587-020-0439-x\n\n' +
             '* Software dependencies\n' +

nextflow.config

@@ -308,8 +308,8 @@ manifest {
     description     = """Taxonomic classification and profiling of shotgun metagenomic data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '1.1.0dev'
-    doi             = ''
+    version         = '1.1.0dev'
+    doi             = '10.5281/zenodo.7728364'
 }
 
 // Load modules.config for DSL2 module specific options

subworkflows/local/standardisation_profiles.nf

@@ -33,7 +33,9 @@ workflow STANDARDISATION_PROFILES {
                             .groupTuple ()
                             .map { [ it[0], it[1].flatten() ] }
 
-    TAXPASTA_MERGE (ch_input_for_taxpasta, [], [])
+    ch_taxpasta_tax_dir = params.taxpasta_taxonomy_dir ? Channel.fromPath(params.taxpasta_taxonomy_dir, checkIfExists: true).collect() : []
+
+    TAXPASTA_MERGE (ch_input_for_taxpasta, ch_taxpasta_tax_dir, [])
 
     /*
         Split profile results based on tool they come from